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#-----------------------------------------------------------------------------
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# PACKAGE : Bio::Root::Xref.pm
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# AUTHOR : Steve Chervitz (sac@bioperl.org)
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# REVISION: $Id: Xref.pm,v 1.8 2002/01/23 11:30:22 heikki Exp $
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# WARNING: This is considered an experimental module.
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# Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved.
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# This module is free software; you can redistribute it and/or
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# modify it under the same terms as Perl itself.
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#-----------------------------------------------------------------------------
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package Bio::Root::Xref;
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use Bio::Root::Global;
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use Bio::Root::Object ();
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use Bio::Root::Vector ();
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@Bio::Root::Xref::ISA = qw( Bio::Root::Vector Bio::Root::Object );
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use vars qw($ID $VERSION);
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$ID = 'Bio::Root::Xref';
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Bio::Root::Xref - A generic cross-reference object.
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B<WARNING: This module is still in the experimental phase and has not been tested.>
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=head2 Object Creation
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use Bio::Root::Object;
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$myObj->xref($object_ref);
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=head2 Object Manipulation
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---------------------------------------------------------------------
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obj() - Get the cross-referenced object.
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desc() - Description of the nature of the cross-reference.
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set_desc() - Set description.
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type() - Symmetric or assymetric.
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---------------------------------------------------------------------
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clear() - remove all cross-references within the Xref object (not implemented).
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An instance of B<Bio::Root::Xref.pm> manages sets of objects not
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necessarily related by inheritance or composition, but by an arbitrary
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criterion defined by the client. Currently, Bio::Root::Xref inherits
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from both B<Bio::Root::Object.pm> and B<Bio::Root::Vector.pm>. An Xref
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object is an example of a heterogeneous Vector object since different
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objects in the vector need not all derive from the same base class.
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The two objects involved in the cross-reference typically involve a
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symmetrical relationship in which each will have a Xref object relating it
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to the other object. This relationship is not necessarily transitive,
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however: if A is an xref of B and B is an xref of C, A is not
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necessarily an xref of C. Assymetric Xrefs are also possible.
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The establishment of cross-references is managed by B<Bio::Root::Object.pm>.
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See the xref() method in that module.
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B<The API for this module is not complete since the module is under development. Caveat emptor.>
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Bio::Root::Object.pm - Core object
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Bio::Root::Global.pm - Manages global variables/constants
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http://bio.perl.org/Projects/modules.html - Online module documentation
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http://bio.perl.org/ - Bioperl Project Homepage
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User feedback is an integral part of the evolution of this and other Bioperl modules.
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Send your comments and suggestions preferably to one of the Bioperl mailing lists.
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Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/MailList.shtml - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and
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their resolution. Bug reports can be submitted via email or the web:
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bioperl-bugs@bio.perl.org
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http://bio.perl.org/bioperl-bugs/
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Steve Chervitz E<lt>sac@bioperl.orgE<gt>
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See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
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Bio::Root::Xref.pm, 0.01 pre-alpha
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Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved.
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This module is free software; you can redistribute it and/or
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modify it under the same terms as Perl itself.
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Update documentation to work with pod2html from Perl 5.004.
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#### END of main POD documentation.
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#####################################################################################
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#####################################################################################
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my( $self, %param ) = @_;
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$self->SUPER::_initialize(%param);
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$self->{'_obj'} = ($param{-OBJ} || undef);
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## By default, all Xrefs are symmetric.
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## Create symmetric cross-reference in obj.
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$self->{'_obj'}->xref(-OBJ=>$param{-PARENT});
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$self->{'_type'} = 'sym';
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$self->{'_type'} = 'asym';
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#####################################################################################
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#####################################################################################
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sub obj {my ($self) = shift; return $self->{'_obj'}; }
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sub desc {my ($self) = shift; return $self->{'_desc'}; }
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sub type {my ($self) = shift; return $self->{'_type'}; }
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sub set_desc {my ($self,$desc) = @_;
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$self->{'_desc'} = $desc;
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## Not implemented. Need to do this carefully.
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## Not sure if this method is needed.
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#####################################################################################
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#####################################################################################
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_obj : The object being cross-referenced to the parent.
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_type : Symmetric or asymmetric
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_desc : Description associated with the cross-reference
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INHERITED DATA MEMBERS (from Bio::Root::Object)
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_parent : The object receiving the cross-reference.
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_name : Descriptive nature of the cross-reference.
added
removed
Bio/Root/Xref.pm
